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In 2011, a particular strain of Escherichia coli bacteria wreaked havoc in Germany. Known as E. coli O104:H4, the pathogen killed 53 people and landed hundreds of others in hospitals. The strain was clearly atypical, and findings by a team of scientists that includes HHMI investigator Matthew Waldor, of Boston’s Brigham and Women’s Hospital, suggest why.

In animals and plants, methylation—the addition of a chemical methyl group to DNA—can turn genes on and off. When the researchers compared DNA from E. coli O104:H4 to that of other strains, they noticed certain genes were methylated differently. Closer inspection showed a virus called a bacteriophage had infected the E. coli, bringing with it a methylating protein.

Using a technique called single-molecule real-time DNA sequencing, the researchers mapped the methylation patterns of E. coli O104:H4. They discovered that not only did the phage add thousands of methylation sites to the pathogen’s genome, it also altered expression patterns of more than a third of its genes—including several essential for growth and mobility. The team published the work December 2012 in Nature Biotechnology.

Waldor says the findings will help researchers understand the role of methylation in the bacteria’s life cycles, infectivity, and perhaps even drug resistance.